User: stu111538

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stu11153860
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Posts by stu111538

<prev • 13 results • page 1 of 2 • next >
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Comment: C: RNA-Seq time series analysis using ImpulseDE2 software
... Ok, actually this is good to know. However, what I meant with missing data was that data for a whole time point for one or more patients is missing. I think the manual extract means missing data in terms of count data for particular genes are missing. To your question: As I understood it from the ...
written 4 weeks ago by stu11153860
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RNA-Seq time series analysis using ImpulseDE2 software
... Hi, I want to use ImpulseDE2 software to identify genes that are differentially expressed over time (I have samples from 12 patients at 4 time points). I have two questions and unfortunately trying to contact the developers failed. 1) Does somebody know whether ImpulseDE2 can deal with missing dat ...
missing data impulsede2 rna-seq transient genes written 6 weeks ago by stu11153860
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Comment: C: RNA-Seq time series analysis using a DESeq2 spline approach yields far too many
... Thank you! Yes, I considered a two-variable model already. I will try this. ...
written 7 weeks ago by stu11153860
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Comment: C: RNA-Seq time series analysis using a DESeq2 spline approach yields far too many
... Thank you Charles Warden for your comment! I will try other approaches to see whether there are just that many differences between my two conditions. Thanks for the link, I though about batch effects, but actually I did not see batches in a PCA. In this special case, I cannot use fold-change as furt ...
written 9 weeks ago by stu11153860
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Comment: C: RNA-Seq time series analysis using a DESeq2 spline approach yields far too many
... I do not think that one would expect 40% of all tested genes being significant in my setting comparing to types of skin biopsies with each other. Maybe if you compare different cell types or tumor vs. healthy cells. ...
written 9 weeks ago by stu11153860
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RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
... Hi, I performed RNA-Seq time series analysis on my set of 12 patients under therapy. Since I only have 5 time points (and for some patients only 4 time points), I decided not to use ImpulseDE2 software, but the DESeq2 spline approach (using 3 splines) the ImpulseDE2 developers used in their benchma ...
time series deseq2 rna-seq splines written 9 weeks ago by stu11153860
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Comment: C: Should I include ambiguously mapped reads in the realignment around InDels?
... in the second part, did I understand you correctly that when I run RealignerTargetCreator, this software starts with those filters you listed and after it does the actual target creation? Thanks! ...
written 15 months ago by stu11153860
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Should I include ambiguously mapped reads in the realignment around InDels?
... Hi, I am wondering whether ambiguously mapped reads (=not uniquely mapped reads, mapping quality 0) do play any role when I perform realignment around InDels (as for example using GATK IndelRealigner or, as in my case, BisSNP BisulfiteIndelRealigner). I performed the alignment of my RRBS data using ...
alignment written 15 months ago by stu11153860 • updated 15 months ago by Medhat8.2k
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Comment: C: How to handle the whole genome sequencing data using by plink?
... You could try Plink 1.9. Command is probably the same: ./plink --vcf your_vcf --make-bed --out ... And try the --memory option as it was suggested. 1. You can merge vcf files using bcftools merge. Before, you have to bgzip and index (tabix) your vcf files. Consider, that your multi-sample vcf will ...
written 2.6 years ago by stu11153860
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Answer: A: How to handle the whole genome sequencing data using by plink?
... Do you want to have all 421 datasets in one ped file? I handled large data with plink recently. I merged 60 vcf files to a multi-sampel vcf. There were 900 million markers and conversion to plink format using Plink 1.9 worked with 100GB MEM und 4 cpus. However, with 70GB it did not work. And you hav ...
written 2.6 years ago by stu11153860

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Scholar 2.5 years ago, created an answer that has been accepted. For A: How to handle the whole genome sequencing data using by plink?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: How to handle the whole genome sequencing data using by plink?

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